Author: scooter
Date: 2012-12-18 13:26:07 -0800 (Tue, 18 Dec 2012)
New Revision: 31019
Modified:
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/TanimotoScorerTask.java
Log:
Fix bugs in tanimoto scoring
Modified: csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
===================================================================
--- csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
2012-12-18 19:41:17 UTC (rev 31018)
+++ csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
2012-12-18 21:26:07 UTC (rev 31019)
@@ -491,6 +491,7 @@
}
} catch (Exception e) {
logger.warning("Error calculating fingerprint:
"+e);
+ e.printStackTrace();
}
}
return fingerPrint;
@@ -967,10 +968,10 @@
return null;
}
- iMolecule = new Molecule(intostruct.getAtomContainer());
+ IMolecule molecule = new
Molecule(intostruct.getAtomContainer());
// Use the molecule to create a SMILES string
SmilesGenerator sg = new SmilesGenerator();
- return sg.createSMILES(iMolecule);
+ return sg.createSMILES(molecule);
} catch (Exception e) {
logger.warning("Structure generation failed: " +
e.getMessage(), e);
return null;
Modified:
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/TanimotoScorerTask.java
===================================================================
---
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/TanimotoScorerTask.java
2012-12-18 19:41:17 UTC (rev 31018)
+++
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/tasks/TanimotoScorerTask.java
2012-12-18 21:26:07 UTC (rev 31019)
@@ -114,19 +114,33 @@
if (settingsDialog != null)
tcCutoff = settingsDialog.getTcCutoff();
+ int nThreads = Runtime.getRuntime().availableProcessors()-1;
+ int maxThreads = settingsDialog.getMaxThreads();
+ if (maxThreads > 0)
+ nThreads = maxThreads;
+
objectCount = 0;
totalObjects = selection.size();
List<CyEdge> edgeList = Collections.synchronizedList(new
ArrayList<CyEdge>());
- updateMonitor();
+ if (nThreads == 1)
+ updateMonitor();
+ // To avoid concurrancy issues, we need to split this up into
two parts. First,
+ // create the structures for all of our compounds
+ List<Compound> compounds = getCompounds(selection,
Cytoscape.getNodeAttributes(),
+
settingsDialog.getCompoundAttributes("node",AttriType.smiles),
+
settingsDialog.getCompoundAttributes("node",AttriType.inchi),
maxThreads);
+
List<CalculateTanimotoTask> taskList = new
ArrayList<CalculateTanimotoTask>();
for (int index1 = 0; index1 < totalObjects; index1++) {
CyNode node1 = (CyNode)selection.get(index1);
if (canceled) break;
- setStatus("Calculating tanimoto coefficients for
"+node1.getIdentifier());
+ if (nThreads == 1)
+ setStatus("Calculating similarities for
"+node1);
+
for (int index2 = 0; index2 < index1; index2++) {
if (canceled) break;
CyNode node2 = (CyNode)selection.get(index2);
@@ -134,14 +148,15 @@
if (node2 == node1)
continue;
- taskList.add(new
CalculateTanimotoTask(origNetwork, node1, node2, tcCutoff));
+ CalculateTanimotoTask task = new
CalculateTanimotoTask(origNetwork, node1, node2, tcCutoff);
+ if (nThreads == 1) {
+ task.call();
+ } else {
+ taskList.add(task);
+ }
}
}
- int nThreads = Runtime.getRuntime().availableProcessors()-1;
- int maxThreads = settingsDialog.getMaxThreads();
- if (maxThreads > 0)
- nThreads = maxThreads;
ExecutorService threadPool =
Executors.newFixedThreadPool(nThreads);
--
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